Depending on just where in the Pacific Northwest your home is located a 90+% furnace may not save enough fuel to cover the additional cost over its lifetime.
I don't know what you might consider as being "pretty decent height" but installing a furnace where it cannot be easily serviced is a big mistake. You need to be sure to adhere to all of the manufacturer's minimum clearances and for ease of service probably exceed the "recommended" clearances for service.
I can't determine just what your plan was concerning the existing chimney but you cannot remove a masonry chimney from the bottom up as the lower part holds the upper part. You would likely need to remove the chimney from the roof down and if you desired to use the roof penetration for the new furnace then you would build a "chimney chase" around the existing penetration to enclose a type B vent, assuming you are using a gas-fired furnace.
The supply and return duct work to your existing duct system would be no small job. Remember that most return ducts are woefully inadequate and that your extensions of both supply and return would likely be larger than the existing ducts.
The blown in insulation would be far more than just an inconvenience, it would have to be contained, likely by building a furnace room enclosure and that too would be a restriction for installation and servicing of the furnace. You also need to make provisions for the entrance of combustion air to this furnace enclosure.
In all of this planning you MUST take into consideration your local mechanical and energy codes. Moving a furnace absolutely requires a permit and inspection by the local Authority Having Jurisdiction.